Biomedical subjects

Yu-Chung Chang

Publications and source records attributed to Yu-Chung Chang.

14 recordsLinked to original sources

PubMed2006

VNTRDB: a bacterial variable number tandem repeat locus database.

Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at http://vntr.csie.ntu.edu.tw/.

Bacteria↗

PubMed2006

Demonstration of fiber-laser-produced plasma source and application to efficient extreme UV light generation.

Efficient generation of extreme UV (EUV) light at lambda = 13.5 nm from a bulk Sn target has been demonstrated by using a fiber laser. The conversion efficiency from the 1064 nm IR to the EUV was measured to be around 0.9% into 2pi steradians within a 2% bandwidth. To the best of our knowledge, this is the first time an all-fiber system was used to generate EUV or soft x rays.

Journal Article↗

PubMed2006

No debridement is necessary for symptomatic or infected acute necrotizing pancreatitis: delayed, mini-retroperitoneal drainage for acute necrotizing pancreatitis without debridement and irrigation.

We sought to determine if necrosectomy can be omitted for complicated acute necrotizing pancreatitis (ANP). Since 1996, we prospectively performed retroperitoneal drainage by introducing a sump drain to the pancreatic head area via a small left flank incision without debridement and irrigation on 19 consecutive complicated ANP patients. We purposely delayed surgery until liquefaction of retroperitoneal tissue reached the left flank. Our patients had a mean Ranson's and APACHE II score of 5.9 (range, 4-8) and 20.1(range, 4-45), respectively. Sixteen available CT showed retroperitoneal liquefaction after 21.3 days (range, 14-26). Operations were delayed for 4.7 weeks (range, 1.3-9.0). No patient succumbed during this period. The indications were infected necrosis in 16 and severe abdominal pain/food intolerance in 3 patients. Average skin incision was 4.0 cm (range, 3-9). Fungi or bacteria were cultured in 15 patients (80.0%). The recovery courses were surprisingly uneventful. Oral intake began within 2.4 days (range, 1-5) and mean hospital stay (16 survivals) was 23.2 days (range, 4-120) after operation. Drains were completely removed 120.6 days (range, 60-250) later from these outpatients. One gastric perforation and one minor duodenal leak were the only procedure-related complications (10.5%). Three patients died (15.8%), although one had a healed ANP. In conclusion, this delay-until-liquefaction strategy without necrosectomy is an easy and effective treatment method.

Aged, 80 and over↗

PubMed2006

Simplified hepatic resections with the use of a Chang's needle.

OBJECTIVE: To demonstrate the use of Chang's needle for hepatic resections. SUMMARY BACKGROUND DATA: Specialized instruments, fine surgical skills, and good control of hepatic inflow and backflow are essential for hepatic resections. This needle was specifically designed to simplify these requirements. METHODS: Whole-thickness interlocking sutures of the liver can first be made along the designed resection line with a Chang's needle; then parenchyma transection can follow without inflow or backflow control. This was consecutively performed on 69 patients with primary (41), metastatic (10), and benign (18) diseases since 1997. RESULTS: Blood loss during parenchyma transection was reduced in 11 right lobectomies (652 mL), 1 3-segmentectomy (300 mL), 14 bisegmentectomies (252 mL), 7 segmentectomies (104 mL), 12 subsegmentectomies (19 mL), 5 wedge resections (7 mL), 18 left lateral segmentectomies (110 mL), and 1 hepatorrhaphy (minimal). There was no procedure-related mortality. A mild bile leakage occurred in 1 case (1.5%) but healed spontaneously. CONCLUSIONS: The preliminary results demonstrate that this maneuver is a simple, easy, and safe method for performing hepatic resections.

Blood Loss, Surgical↗

PubMed2006

Database to dynamically aid probe design for virus identification.

Viral infection poses a major problem for public health, horticulture, and animal husbandry, possibly causing severe health crises and economic losses. Viral infections can be identified by the specific detection of viral sequences in many ways. The microarray approach not only tolerates sequence variations of newly evolved virus strains, but can also simultaneously diagnose many viral sequences. Many chips have so far been designed for clinical use. Most are designed for special purposes, such as typing enterovirus infection, and compare fewer than 30 different viral sequences. None considers primer design, increasing the likelihood of cross hybridization to similar sequences from other viruses. To prevent this possibility, this work establishes a platform and database that provides users with specific probes of all known viral genome sequences to facilitate the design of diagnostic chips. This work develops a system for designing probes online. A user can select any number of different viruses and set the experimental conditions such as melting temperature and length of probe. The system then returns the optimal sequences from the database. We have also developed a heuristic algorithm to calculate the probe correctness and show the correctness of the algorithm. (The system that supports probe design for identifying viruses has been published on our web page http://bioinfo.csie.ncu.edu.tw/.)

Algorithms↗

PubMed2005

Emulsion intercalation of smectite clays with comb-branched copolymers consisting of multiple quaternary amine salts and a poly(styrene-butadiene-styrene) backbone.

Layered silicates were intercalated with comb-branched copolymers consisting of a hydrophobic polystyrene-b-poly(ethylene/butylene)-b-polystyrene (SEBS) backbone and multiple pendants of poly(oxyalkylene) (POA) quaternary ammonium salts. The requisite intercalating agents were synthesized by grafting POA amines on the maleated SEBS. The corresponding SEBS-POA amine salts were found to have two functions, the capability to emulsify toluene/water mixtures to fine particle sizes of 60-70 nm in diameter and to exchange ions with sodium montmorillonite. The resulting silicate hybrids were characterized by X-ray diffraction and transmission electron microscopy. Two types of intercalations with silicate d spacing of 18 and 50 A were obtained, in which the dissimilarity is attributed to disparate polymer incorporations, POA pendants only or the combination of both the SEBS backbone and POA in the gallery. Furthermore, the two conformations of polymer-intercalated silicates are reversibly transformable by varying emulsion conditions, micelle sizes, and solvents.

Journal Article↗

PubMed2005

High-energy and high-peak-power nanosecond pulse generation with beam quality control in 200-microm core highly multimode Yb-doped fiber amplifiers.

We explored high-energy and high-peak-power pulse generation in large-core multimode fiber amplifiers, achieving what is to our knowledge the highest reported energies, up to 82 mJ for 500-ns pulses, 27 mJ for 50-ns pulses, and 2.4-MW peak power for 4-ns pulses at 1064 nm, using 200-microm-diameter and 0.062-N.A. core Yb-doped double-clad fiber amplifiers. The highly multimode nature of the fiber core was mitigated by use of a coiling-induced mode-filtering effect to yield a significant improvement in output-beam quality from M2 = 25 from an uncoiled fiber to M2 = 6.5 from a properly coiled fiber, with the corresponding reduction in number of propagating transverse modes from > or = 200 to < or = 20.

Journal Article↗

PubMed2005

SpliceInfo: an information repository for mRNA alternative splicing in human genome.

We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.

Alternative Splicing↗

PubMed2004

i-Genome: a database to summarize oligonucleotide data in genomes.

BACKGROUND: Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. RESULTS: The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. CONCLUSIONS: This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

Alu Elements↗

PubMed2002

Variation of hepatitis C virus load, hypervariable region 1 quasispecies and CD81 hepatocyte expression in hepatocellular carcinoma and adjacent non-cancerous liver.

Hepatitis C virus (HCV) infection is etiologically associated with the development of hepatocellular carcinoma (HCC) worldwide. HCV has been reported to exist and replicate in both HCC and adjacent non-cancerous liver tissue, but limited information was available on HCV viral load and quasispecies composition in HCC relative to adjacent non-cancerous hepatocytes. Previous study has also suggested CD81, a surface hepatocyte protein, as a receptor for HCV. To clarify the above, HCV-RNA and CD81-RNA titers in 20 paired hepatectomized liver and serum were quantitatively measured by chemiluminescent RT-cPCR. Hypervariable region 1 (HVR-1) variations of parallel specimens were analyzed after subcloning in 6 patients. HCV-RNA levels in serum and non-cancerous liver were markedly higher for HCV genotype 1 than genotype non-1. HCV levels were markedly higher in non-cancerous liver than in HCC (P = 0.001) in a genotype-independent manner, with a mean ratio of 56:1 for non-cancerous tissue to HCC. Both non-cancerous and HCC tissues had the same level of CD81-RNA expression, which was not linked to HCV load. HCV-RNA quantity in both HCC and non-cancerous liver correlated with the number of HVR-1 quasispecies in the tissue, and distinct HVR-1 subclones existed.

Adult↗

PubMedDate not supplied

Overexpression of c-erb-B2 proteins in tumor and non-tumor parts of gastric adenocarcinoma--emphasis on its relation to H. pylori infection and clinicohistological characteristics.

BACKGROUND/AIMS: This study was designed to test whether c-erb-B2 overexpression can be related to H. pylori infection or clinicohistological characteristics of patients with gastric cancers. METHODOLOGY: One hundred patients with gastric cancer were included. Their gastric specimens were evaluated for the presence of H. pylori infection and overexpression of c-erb-B2 on both tumor and non-tumor mucosa. The clinicohistological characteristics, including stage, histological subtype, cell differentiation, and locations of gastric cancer were reviewed. RESULTS: Seventy-five patients (75%) had H. pylori infection. The H. pylori infection rate was higher in the patients with non-cardiac cancers than those with cardiac cancers (87.5% vs. 25%, P < 0.05), higher in the patients with intestinal-type cancers than those with diffuse-type cancers (78.8% vs. 53.3%, P < 0.05). The overexpression of c-erb-B2 on gastric cancers was not significantly different between patients with and without H. pylori infection (30.7% vs. 36%, P = NS). Overexpression of c-erb-B2 on the gastric cancer tissues increased as the tumor stage turned upward (stage I: 10%; II: 23.3%, III: 32.5%, IV: 55%, P < 0.05), and highest in the poorly differentiated cancers (56.6%). Only patients with advanced stages as II to IV had c-erb-B2 overexpression on the non-tumor part of stomach (P < 0.05). CONCLUSIONS: H. pylori infection is closely related with the non-cardiac, intestinal-type gastric cancers, but not with the c-erb-B2 overexpression on the gastric cancer. As c-erb-B2 overexpression on gastric cancer is significantly related with poor tumor differentiation and advanced stage, and it thus implicates a poor prognosis and late event of carcinogenesis.

Adenocarcinoma↗

PubMedDate not supplied

Fibrolamellar hepatocellular carcinoma with a recurrence of classic hepatocellular carcinoma: a case report and review of Oriental cases.

A 72-year-old Chinese male, hepatitis B carrier, received a right hepatic trisegmentectomy in 1997 for fibrolamellar hepatocellular carcinoma. Serum alpha-fetoprotein was in the normal range until two years after the operation, a rapid increase to 241 ng/mL occurred and computed tomography showed a 2-cm-sized recurrent nodule in the caudate lobe. Because computed tomography arterioportography showed additional multifocal nodules in the residual liver, transarterial embolization was performed. Four months after the first transarterial embolization, the caudate tumor grew to 6 cm and serum alpha-fetoprotein increased to 6090 ng/mL. Prior to the second transarterial embolization, this new hepatic lesion received a biopsy and showed a characteristic feature of classic hepatocellular carcinoma, which was different from the previous one. Four months after the second transarterial embolization, computed tomography showed no recurrent tumor and serum alpha-fetoprotein subsequently normalized. Twenty-two months after the first transarterial embolization, a 2.5-cm-sized tumor recurred again at the lateral segment. At this time, serum alpha-fetoprotein (3.6 ng/mL) was not elevated. He received the third transarterial embolization and is still alive. Recurrence of fibrolamellar hepatocellular carcinoma after hepatic resection has been reported to be high, but a case report with a character of muticentric, multifocal, and metachronous recurrences of fibrolamellar and classic type hepatocellular carcinoma is very rare. This is the second case report in the literature.

Aged↗

PubMedDate not supplied

Low mortality major hepatectomy.

BACKGROUND/AIMS: A retrospective series of major hepatectomy using a simple strategy. METHODOLOGY: From 1995 to 2002, 104 major hepatectomies were performed, including 16 extended and 35 right/left lobectomies, 11 bisegmentectomies, and 42 left lateral segmentectomies. Seventy-two patients had malignant tumors. Chronic hepatitis was present in 9 and mild to severe cirrhosis in 16 of 47 hepatocellular carcinomas. Intrahepatic duct stone constituted 28 of 32 patients with benign disease. Hilar ligation without pedicle clamp for lobectomy and Pringle's maneuver for segmentectomy were initially our standard procedures. Since 1997, Chang's needle was applied on 34 patients to block hepatic inflow and outflow by entire thickness, interlocking mattress sutures. RESULTS: Three patients (2.9%) died postoperatively. Of the two cholangiocarcinoma patients, one underwent extended right lobectomy and died of multiple organ failure and the other underwent left lateral segmentectomy and died of AMI unrelated to the surgery. One hepatocellular carcinoma patient underwent left lateral segmentectomy and died of hepatic failure. Significant complications (11.5%) included three bile leaks (2.9%), six abscesses (5.8%), one hepatic failure (1%), one ileus (1%), and one ventral hernia (1%). One major bile leak necessitated a reconstructive surgery. CONCLUSIONS: Our strategies for hepatic resection are simple, however we are able to achieve a low mortality major hepatectomy.

Carcinoma, Hepatocellular↗

PubMedDate not supplied

A proposed inflammation grading system for laparoscopic cholecystectomy.

BACKGROUND/AIMS: Currently, there is no comprehensive method to classify the inflammatory status of the GB and Calot's triangle. METHODOLOGY: From 1996, we performed LC on 111 patients with symptomatic gallbladder diseases, irrespective of onset, using an abdominal wall-lifting method. Thirty-six patients had acute cholecystitis, while thirty had chronic cholecystitis. Severe inflammation prompted the author to design a grading system to record inflammatory status and to evaluate the feasibility of LC prospectively. GB with none - mild, moderate, severe wall thickening, and Calot's triangle involvement with mild - moderate, and severe inflammation were classified as Grade I - V, respectively. RESULTS: Forty-six cases had severe inflammation greater than grade III, however, neither CBD injury nor mortality was experienced. Complications were minimal. Of ten conversion cases (9.0%), eight were grade V, one grade III, and one grade I. Poor laparoscopic view caused by incomplete muscle relaxation accounted for four of the conversions. CONCLUSIONS: Our grading system is useful in evaluating feasibility of difficult gallbladders, helping to decide conversion during LC, and as a tool to record or elucidate the chronological inflammatory changes of various GB disorders.

Acute Disease↗